He was born at Stony Stratford, Buckinghamshire, England about 1590, to Rev. Richard Eaton and his wife, Elizabeth.[1] His father may have been the curate at that time, but later became Vicar of Great Budworth, Chester. Theophilus married Grace Hiller, and had at least a daughter (Mary), and a son (Samuel) before her death (some authorities think that he also had a son by the name of James).

In 1625 he remarried, this time to a widow, Anne Yale, who was the daughter of George Lloyd, the Bishop of Chester (some authorities say Anne Morton, the daughter of Bishop Thomas Morton of Chester). The couple had three children (Theophilus, Hannah, and Elizabeth), but the household raised eight children. Besides their three, and Mary and Samuel, it included Anne, David, and Thomas Yale from Anne's first marriage to Thomas Yale.

The three Yale children all had notable places in the history of Connecticut. Thomas Yale (son of Thomas and Ann (Lloyd) Yale, settled in the New Haven Colony and signed the Fundamental Agreement of the New Haven Colony on June 4, 1639. Anne Yale (the daughter) married Edward Hopkins in 1631; he later became the governor of Connecticut. David Yale, who married Ursula Knight in 1641, became the father of Elihu Yale, namesake of Yale College.

Governor Eaton's five children fared as follows. Daughter Mary Eaton married Valentine Hill of Boston in 1647. (His brother, Nathaniel Eaton, the first schoolmaster of Harvard, was present as a witness.) Samuel Eaton married Mabel (Harlakenden) Haynes in 1654. Both of them died in the small pox epidemic of 1655. Hannah Eaton married the Lt. Governor William Jones (1624–1706) in 1659. Theophilus Eaton, Jr., or Ellis, as he was known, returned to England with his mother after his father's death, settled in [[Dublin, Ireland],] and married an Anne King. Elizabeth died in London in March 1637 before the family departed for the colonies.

For several years Theophilus was an agent for King Charles I to the Danish Court, then a merchant in London. He was a Puritan interested in colonial development and was one of the original patent holders and president of the Massachusetts Bay Company.

He emigrated to New England with other Puritans in the ship Hector, arriving in Boston on June 26, 1637.

His group of colonists had John Davenport as their religious leader, and they wanted to start their own settlement – probably due in part to the commanding persona of John Winthrop, Governor of the Massachusetts Bay Colony at the time (1637 to 1640, and many other terms). Winthrop was termed "an object of great fear in all the colonies," and caused the Rev. Thomas Hooker and others to go off and form their own colonies as well.

That fall, Eaton led an exploration to the south, and located a site at Quinnipiack on the northern shore of Long Island Sound. On November 14, 1638, he and his company entered into an agreement with the chief sachemMomauquin agreeing that in exchange for protection from the Quinnipiack Indians' ancient enemies, the Mohawk and the Pequot, Momauquin would relinquish his right, title, and interest to the lands that both parties agreed would not later evolve into feelings of animosity, hate, or regret. [Cf. J. W. Barber, History and Antiquities of New Haven, (Conn.) (1831) pp. 25–29].

The Mohawks and the Pequots had all but wiped out the New Haven Indians, leaving but 40 surviving males, and to that end Theophilus and his company also covenanted to protect them when unreasonably assaulted and terrified, that they would always have a sufficient quantity of land to plant on, and by way of free and thankful retribution that they give to the sachem and his council and company: twelve coats of English cloth, twelve alchemy spoons, twelve hatchets, twelve hoes, two dozen knives, twelve porringers, and four cases of French knives & scissors.

This agreement was signed and legally executed by Momauquin and his council as well as by Theophilus Eaton and John Davenport.

Some still say, however, that Theophilus simply traded thirteen coats to the local Indians for seven townships of land; but what is a fact is that in the following December of 1638 he and his company did also purchase the usage of a large area of land from Monotowese, son of the sachem at Mattabeseck, which was 10 miles in length and 13 in breadth. He did pay 13 coats to Monotowese as per their agreement, but again, the English gave the Indians ample grounds to plant on and free usage of all the lands for hunting. Further, even though Monotowese's tribe consisted of but 10 males with their women and children, it was understood that the English would also protect them from the Mohawk and the Pequots.

Upon arrival in the new colony, Theophilus at first attempted to resume his trade as a merchant. He was not successful, however, since the colony was too new to afford imports and the Indian fur trade was more successful at the Dutch outposts at Hartford, so he soon turned to farming.

When the New Haven Colony established its administration, he was chosen as one of the "seven pillars of the church" acting as one of the 7 councilors who formed the body of freemen and elected civil officers.

He was elected as the first governor on June 4, 1639 and reelected each year until his death on January 7, 1657/8 (Julian Calendar timing). He was buried on the green in New Haven and later his remains were removed to Grove Street Cemetery, New Haven. One of his major accomplishments as governor was the creation of a written legal code for the colony in 1655 later to be known as the Blue Laws of Connecticut.[2] For this, and the fact that he was the first president of the Massachusetts Bay Company, he is sometimes thought of as being the Father of American Law, but this is arguably an example of hyperbole.

Theophilus' younger brother Nathaniel Eaton (1609–1674) was the first schoolmaster of Harvard College. He was deposed in 1639 by the then Governor John Winthrop in what some have considered to be Massachusetts' first Witch Trial. Another brother, Samuel Eaton (1597–1665), was a minister who accompanied Theophilus to New Haven, but later returned to England.